Deputy Interior Secretary Eddy Juarez, who went to area Thursday, told The Associated Press that 17 people have been arrested and there are arrest warrants for at least 30 more.
Earlier Thursday, Interior Secretary Mauricio Lopez Bonilla said security forces had recovered several weapons and shotguns.
Residents remained calm and allowed authorities to enter their homes.
"I don't intervene because I'm poor and I have to work to support my family but the truth is that the mine does affect us when it comes to the environment," said Mariano Lopez Escobar, who lives in Xalapan, and watched as officials raided homes nearby. "Although, it sounds like that with an order from the president for the mine to start working there isn't much one can do."
The emergency decree covers the townships of Jalapa, Mataquescuintla, Casillas and San Rafael Las Rosas in Jalapa and Santa Rosa states. It restricts constitutional rights such as freedom of movement, the right to bear arms, freedom of association and demonstration.
The government ordered it for 30 days, but Guatemalan lawmakers have yet to approve the duration of the state of emergency.
Protesters temporarily detained 23 police officers, seizing their firearms before releasing them. Later, in a nearby town, another officer was shot and killed in a confrontation possibly related to the mine clashes.
Yuri Melini, the director of the Legal Action Center for Human Rights, said "we believe that if crimes have been committed, they should be prosecuted, but the community's legitimate right to oppose the mine should not be criminalized."